The goal of this project is to assess the utility of ion/atom reactions in the elucidation of macromolecular structures that are refractory to the classical approach of collisionally activated dissociation (CAD). The thesis is that the reactivity of radicals such as the free hydrogen atom will stimulate cleavages of a peptide or protein molecule in a non-mass dependent manner, and thereby offer advantages in structure elucidation not achievable by CAD. A Varian Saturn I Ion Trap Mass Spectrometer has been modified to accommodate a microwave generator which will dissociate hydrogen gas into hydrogen atoms for direct injection into the ion trap volume. Other flanges have been mounted on the ion trap vacuum jacket to accommodate the introduction of a small sample probe and a window for laser irradiation to provide MALDI of peptides of up to mass 600 for preliminary studies. Preliminary experiments have shown that we can successfully generate the microwave discharge at sufficiently low pressures to be compatible with the interface to the vacuum system of the ion trap mass spectrometer. In addition, we have demonstrated that successful operation of the ion trap mass spectrometer is not adversely affected by the microwave discharge nor by the high pressure or increased gas load of hydrogen from the microwave discharge interface.